Amyloid diseases are associated with the transformation of normally soluble proteins into amyloid fibrils, which are elongated, unbranched protein aggregates (C. M. Dobson, Trends Biochem Sci 24, 329 (September, 1999); J. D. Sipe, A. S. Cohen, J Struct Biol 130, 88 (June, 2000)). Amyloid fibrils are composed mainly of β-sheets and share common characteristics, including a cross-β x-ray diffraction pattern and characteristic staining by the dye Congo Red (P. Westermark et al., Amyloid 14, 179 (September, 2007)). In Alzheimer's disease patients, two distinct types of fibrillar aggregates are commonly found in brain samples: amyloid plaques comprising deposits of amyloid beta protein (Aβ) and neurofibrillary tangles consisting of the microtubule-associated protein tau (D. J. Selkoe, Physiol Rev 81, 741 (April, 2001)). Tau filaments bind the dye thioflavine S (ThS) and yield fluorescent signal and have a cross-beta diffraction pattern (J. Berriman et al., Proc Natl Acad Sci USA 100, 9034 (Jul. 22, 2003); P. Friedhoff, A. Schneider, E. M. Mandelkow, E. Mandelkow, Biochemistry 37, 10223 (Jul. 14, 1998)). The association of tau with several diseases including Alzheimer's disease and senile dementia makes it an important target for disrupting fibrillation (J. Avila, FEBS Lett 476, 89 (Jun. 30, 2000)). Though recent studies suggest that small oligomers may be the pathogenic species in amyloid disease, agents that disrupt fibril formation have been shown to reduce cytotoxicity (A. Kapurniotu, A. Schmauder, K. Tenidis, J Mol Biol 315, 339 (Jan. 18, 2002); M. Cruz et al., J Pept Res 63, 324 (March, 2004)).
Because of the association of fibrils with disease, there have been several attempts at delaying and preventing fibril formation. Other proposed strategies involve small molecules (Ferrao-Gonzales et al., 2005; Ono et al., 2004; Ono et al., 2004; Ono et al., 2002; Ono et al., 2004), peptides (Tjemberg et al., 1996), and peptide variants (Cruz et al., 2004; Doig et al., 2002; Harkany et al., 1999; Kapurniotu et al., 2002; Tatarek-Nossol et al., 2005; Tjernberg et al., 1997; Wiesehan et al., 2003). These methods include using short peptide segments from the fibrillating protein (L. O. Tjernberg et al., J Biol Chem 271, 8545 (Apr. 12, 1996)) and variants of these peptides. The peptide variants include N-methylated backbones (E. Hughes, R. M. Burke, A. J. Doig, J Biol Chem 275, 25109 (Aug. 18, 2000); A. Kapurniotu, A. Schmauder, K. Tenidis, J Mol Biol 315, 339 (Jan. 18, 2002); D. J. Gordon, K. L. Sciarretta, S. C. Meredith, Biochemistry 40, 8237 (Jul. 27, 2001)), modified N- and C-termini (M. A. Findeis et al., Biochemistry 38, 6791 (May 25, 1999)), and D-amino acid peptides (C. Soto, M. S. Kindy, M. Baumann, B. Frangione, Biochem Biophys Res Commun 226, 672 (Sep. 24, 1996)). These empirical approaches are not as yet successful.
Structure-based design of amyloid fibril inhibitors has been a challenging problem. Previous structure-based approaches to prevent fibrillation have addressed only the stabilization of the native structure (Klabunde et al., 2000; Petrassi et al., 2005; Petrassi et al., 2000). This approach is not applicable to misfolding diseases in which the proteins, including tau, are thought to lack an ordered, native structure.
There remains a need in the art for improved inhibitors of fibril formation, in particular those designed using a rational structure-based approach.